#!/bin/bash -e

function info() {
echo Usage: `basename $0` 'in.vcf'
exit 65
}

while getopts ":p:l:mgh" opts
do
case $opts in
	m) somatic=T;;
	g) single_cell=T;;
	l) interval=$OPTARG;;
	p) out_prefix=$OPTARG;;
	\?) info;;
esac
done
shift $(($OPTIND - 1))

test $# -lt 1 && info


. $var

echo;echo;echo gatk SelectVariants
java $tmp -jar $gatk \
	-R $ref_genome \
    -T SelectVariants \
    -V $1 \
    -o $out_prefix.select.vcf \
    -select 'set == "Intersection"'
    
. $cmd_done